In spite of the difficulties, the Lord abandons the idea of destroying the unproductive trees, instead bending his efforts to the task of saving the essence of all of them. While the process will allow the destruction of some parts of each type of tree, yet the Lord will salvage the good from each and bring them all back together.
Certainly this aspect of the allegory is clear. Yahweh will save all of his children who choose to turn to the Lord. Even though we may have strayed as a group, nevertheless, the Lord will continually strive to save all he can and to bring them back to his one gospel.